Related papers: Facilitated diffusion on mobile DNA: configuration…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of…
In this letter, we characterize experimentally the diffusiophoretic motion of colloids and lambda- DNA toward higher concentration of solutes, using microfluidic technology to build spatially- and temporally-controlled concentration…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics (MD) simulations. It is observed that dependence of the reduced diffusion coefficient of these…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…